MSc | Bioinformatician at Institut Josep Carreras

Biotechnologist with training in Molecular Genetics and Bioinformatics. Interested in omics data analysis to study the mechanisms of gene regulation in mammals. See more about me on my website.

PhD student

Institut Germans Trias i Pujol & Institut Josep Carreras

Badalona, Spain

11/2022 - Present

Group of Regulatory Genomics (Dr. Tanya Vavouri)
Study of the role of transposable elements in the evolution of gene regulation in mammals.

Bioinformatician & master’s thesis student

Institut Josep Carreras

Badalona, Spain

08/2021 - 11/2022

Group of Regulatory Genomics (Dr. Tanya Vavouri)
Study of Piwi-interacting RNAs (piRNAs), their biogenesis mechanisms and their conservation across species.

• Analysis and integration of small RNA-seq, RNA-seq and genomic data.
• Development of a method for differential expression without gene length differences when using multiple species.
• Mentoring of bachelor’s and master’s thesis students.
• Master’s thesis (UOC): Analysis of the variation in piRNA expression across three Mus species.

Bioinformatician

Istituto Europeo di Oncologia

Milan, Italy

07/2019 - 07/2021

Group of Epigenetic Mechanisms in Cancer (Dr. Diego Pasini)
Study of Wnt/\(\beta\)catenin signaling pathway -and others- and its effects in transcription and epigenetic modifications in the context of colorectal cancer and stem cell development.

• Analysis and integration of omics data (RNA-/ChIP-/ATAC-seq).
• Comparison of different ATAC-seq peak callers.
• Comparison of different sequencing depths for RNA-seq and their influence in differential expression analysis.

Master’s thesis student & Research assistant

Instituto de Biomedicina de Sevilla

Seville, Spain

09/2017 - 10/2018

Group of Gene Expression (Dr. Sebastián Chávez)
Study of Xrn1 and Ccr4 roles in yeast nucleosome architecture and gene transcription.

• Analysis of MNase-seq data from Xrn1-, Ccr4-mutant and WT yeast strains.
• Perform MNase-qPCR experiments, including MNase DNA digestion, primer desing, qPCRs and analysis.
• Master’s thesis (US): Influence of Xrn1 in nucleosome positioning […] and its effects in transcription.

Internship student

Institut d’Investigació Biomèdica de Girona

Girona, Spain

07/2017 - 09/2017

Unit of Diabetes, Endocrinology and Nutrition
Extracurricular internship. Identification of novel factors (genetic and bacterial) related to adipose tissue physiology and obesity.

• RNA extraction from mouse hepatic biopsies.
• DNA extraction from human feces to study the composition of the microbiota.

Internship & bachelor’s thesis student

Microbial. Sistemes i aplicacions analítiques, S.L.

Girona, Spain

09/2016 - 06/2017

Microbiological and molecular analyses of food and water for pathogen detection and food forensics | Study of butyrate effects on the ileal microbiota of colectomized colorectal cancer patients.

• DNA extraction of intestinal mucosa biopsies.
• (q)PCR experiments to detect clusters and families of bacteria.
• NGS data analysis to quantify bacterial genera in intestinal biopsies.
  
• Bachelor’s thesis (UdG): Butyrate-induced changes in the […] microbiota in colorectal cancer patients […].

PhD in Bioinformatics

Universitat Autònoma de Barcelona (UAB)

Barcelona, Spain

2022 - Present

• INPhINIT Incoming PhD Fellowship from LaCaixa.
• Research carried out at Regulatory Genomics group of the Institut Josep Carreras (IJC).

MSc in Bioinformatics and Biostatistics

Universitat Oberta de Catalunya (UOC)

Online

2018 - 2022

• Focused on Computational Genomics.
• Master’s thesis: Analysis of the variation in piRNA expression across three close related Mus species. Grade: 9.7/10 (with honours). Supervisor: Dr. Tanya Vavouri
• Overall grade: 8.94/10.

MSc in Molecular Genetics and Biotechnology

Universidad de Sevilla (US)

Seville, Spain

2017 - 2018

• Specialization in Molecular Biology Research.
• Master’s thesis: Influence of Xrn1 in nucleosome positioning across Saccharomyces cerevisiae genome and its effects in transcription. Grade: 9.2/10. Supervisors: Dr. Sebastián Chávez de Diego & Dr. Gabriel Gutiérrez Pozo.
• Overall grade: 9.33/10.

BSc in Biotechnology

Universitat de Girona (UdG)

Girona, Spain

2012 - 2017

• Specialization in Cellular & Molecular Biotechnology.
  
• Bachelor’s thesis: Butyrate-induced changes in the diversity of intestinal mucosa-associated microbiota in colorectal cancer patients submitted to a lateral ileostomy. Grade: 9.4/10. Supervisor: Prof. Jesús García-Gil
• Overall grade: 8.12/10.

Begley et al. Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration. RNA Biology. 2021. doi: 10.1080/15476286.2020.1845504

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Mitjavila & Vavouri. Analysis of piRNA variation across three Mus species (in Catalan). Oral presentation at the Jornades de Biologia de la Reproducció from the Catalan Society of Biology (March 2022)

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